RubyGems - pione - Versions diffs - 0.5.0.alpha.2 → 0.5.0 - Mend

pione 0.5.0.alpha.2 → 0.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (65) hide show

data/example/MakePair/scenario/case2/pione-scenario.json CHANGED

@@ -2,21 +2,21 @@
   "ScenarioName": "case2",
   "ParamSet": null,
   "Inputs": [
-    "input/9.i",
     "input/10.i",
-    "input/11.i"
+    "input/11.i",
+    "input/9.i"
   ],
   "Outputs": [
-    "output/perm-9-11.pair",
-    "output/succ-10-11.pair",
-    "output/perm-11-9.pair",
-    "output/perm-10-11.pair",
+    "output/comb-10-11.pair",
     "output/comb-9-10.pair",
     "output/comb-9-11.pair",
-    "output/comb-10-11.pair",
-    "output/succ-9-10.pair",
-    "output/perm-11-10.pair",
+    "output/perm-10-11.pair",
     "output/perm-10-9.pair",
-    "output/perm-9-10.pair"
+    "output/perm-11-10.pair",
+    "output/perm-11-9.pair",
+    "output/perm-9-10.pair",
+    "output/perm-9-11.pair",
+    "output/succ-10-11.pair",
+    "output/succ-9-10.pair"
   ]
 }

data/example/MakePair/scenario/case3/pione-scenario.json CHANGED

@@ -2,42 +2,42 @@
   "ScenarioName": "case3",
   "ParamSet": null,
   "Inputs": [
-    "input/9.i",
-    "input/5.i",
+    "input/1.i",
     "input/3.i",
+    "input/5.i",
     "input/7.i",
-    "input/1.i"
+    "input/9.i"
   ],
   "Outputs": [
-    "output/perm-5-1.pair",
-    "output/perm-7-1.pair",
+    "output/comb-1-3.pair",
+    "output/comb-1-5.pair",
+    "output/comb-1-7.pair",
+    "output/comb-1-9.pair",
+    "output/comb-3-5.pair",
+    "output/comb-3-7.pair",
+    "output/comb-3-9.pair",
+    "output/comb-5-7.pair",
+    "output/comb-5-9.pair",
+    "output/comb-7-9.pair",
+    "output/perm-1-3.pair",
+    "output/perm-1-5.pair",
+    "output/perm-1-7.pair",
+    "output/perm-1-9.pair",
     "output/perm-3-1.pair",
-    "output/perm-9-5.pair",
+    "output/perm-3-5.pair",
     "output/perm-3-7.pair",
-    "output/comb-3-9.pair",
     "output/perm-3-9.pair",
-    "output/perm-7-9.pair",
-    "output/perm-1-3.pair",
+    "output/perm-5-1.pair",
+    "output/perm-5-3.pair",
     "output/perm-5-7.pair",
-    "output/perm-9-1.pair",
-    "output/comb-1-9.pair",
-    "output/perm-7-5.pair",
-    "output/perm-1-7.pair",
-    "output/comb-1-7.pair",
-    "output/perm-1-5.pair",
-    "output/comb-1-3.pair",
     "output/perm-5-9.pair",
+    "output/perm-7-1.pair",
     "output/perm-7-3.pair",
-    "output/perm-9-7.pair",
-    "output/perm-5-3.pair",
-    "output/comb-5-7.pair",
-    "output/perm-1-9.pair",
-    "output/comb-3-7.pair",
-    "output/perm-3-5.pair",
-    "output/comb-7-9.pair",
+    "output/perm-7-5.pair",
+    "output/perm-7-9.pair",
+    "output/perm-9-1.pair",
     "output/perm-9-3.pair",
-    "output/comb-1-5.pair",
-    "output/comb-3-5.pair",
-    "output/comb-5-9.pair"
+    "output/perm-9-5.pair",
+    "output/perm-9-7.pair"
   ]
 }

data/example/OddSelector/OddSelector.pione CHANGED

@@ -1,4 +1,3 @@
 Rule OddSelector
   input '*.i'.all
   output '*.res'.all

data/example/OddSelector/pione-package.json CHANGED

@@ -4,8 +4,8 @@
   ],
   "Documents": [
-    "Package.pione",
-    "OddSelector.pione"
+    "OddSelector.pione",
+    "Package.pione"
   ],
   "Scenarios": [
     "scenario"

data/example/OddSelector/scenario/pione-scenario.json CHANGED

@@ -2,22 +2,22 @@
   "ScenarioName": "from 1 to 10",
   "ParamSet": null,
   "Inputs": [
-    "input/9.i",
-    "input/2.i",
+    "input/1.i",
     "input/10.i",
-    "input/5.i",
+    "input/2.i",
     "input/3.i",
+    "input/4.i",
+    "input/5.i",
+    "input/6.i",
     "input/7.i",
     "input/8.i",
-    "input/1.i",
-    "input/6.i",
-    "input/4.i"
+    "input/9.i"
   ],
   "Outputs": [
-    "output/3.res",
-    "output/9.res",
     "output/1.res",
+    "output/3.res",
+    "output/5.res",
     "output/7.res",
-    "output/5.res"
+    "output/9.res"
   ]
 }

data/example/PegasusWMS/Merge/PegasusWMSMerge.pione CHANGED

@@ -1,4 +1,3 @@
 Rule PegasusWMSMerge
   output 'binaries.txt'
 Flow

data/example/PegasusWMS/Merge/PegasusWMSMerge.pnml CHANGED

@@ -41,7 +41,7 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
     </place>
     <place id="p2">
       <name>
-        <text>$DIRS := ("/bin" | "/usr/bin" | "/usr/local/bin").all</text>
+        <text>{DIRS: ("/bin" | "/usr/bin" | "/usr/local/bin").all}</text>
         <graphics>
           <offset x="100" y="290"/>
         </graphics>
@@ -56,7 +56,7 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
     </place>
     <place id="p1">
       <name>
-        <text>$INDEX := 0.upto(2)</text>
+        <text>{INDEX: 0.upto(2)}</text>
         <graphics>
           <offset x="100" y="210"/>
         </graphics>

data/example/PegasusWMS/Pipeline/PegasusWMSPipeline.pione CHANGED

@@ -1,4 +1,3 @@
 Rule PegasusWMSPipeline
   output 'count.txt'
 Flow

data/example/PegasusWMS/Split/PegasusWMSSplit.pione CHANGED

@@ -1,4 +1,3 @@
 Rule PegasusWMSSplit
   output 'count.txt.*'.all
 Flow

data/example/ScoreAggregation/pione-package.json CHANGED

@@ -11,13 +11,13 @@
     "scenario/case1"
   ],
   "Bins": [
+    "bin/apply-template.rb",
+    "bin/histgram-graph.sh",
     "bin/mean-summary.rb",
     "bin/personal-bar-graph.sh",
     "bin/personal-pre-statistics.rb",
-    "bin/apply-template.rb",
-    "bin/total-statistics.rb",
     "bin/total-mean.rb",
-    "bin/histgram-graph.sh"
+    "bin/total-statistics.rb"
   ],
   "Etcs": [

data/example/ScoreAggregation/scenario/case1/pione-scenario.json CHANGED

@@ -2,32 +2,32 @@
   "ScenarioName": "case1",
   "ParamSet": null,
   "Inputs": [
-    "input/L.score",
-    "input/O.score",
-    "input/R.score",
-    "input/F.score",
-    "input/Y.score",
-    "input/X.score",
-    "input/H.score",
-    "input/J.score",
+    "input/A.score",
     "input/B.score",
-    "input/T.score",
     "input/C.score",
-    "input/V.score",
-    "input/P.score",
-    "input/E.score",
-    "input/I.score",
-    "input/Q.score",
     "input/D.score",
-    "input/W.score",
-    "input/N.score",
-    "input/A.score",
+    "input/E.score",
+    "input/F.score",
     "input/G.score",
-    "input/U.score",
-    "input/Z.score",
+    "input/H.score",
+    "input/I.score",
+    "input/J.score",
     "input/K.score",
+    "input/L.score",
     "input/M.score",
+    "input/N.score",
+    "input/O.score",
+    "input/P.score",
+    "input/Q.score",
+    "input/R.score",
     "input/S.score",
+    "input/T.score",
+    "input/U.score",
+    "input/V.score",
+    "input/W.score",
+    "input/X.score",
+    "input/Y.score",
+    "input/Z.score",
     "input/stat-template.erb"
   ],
   "Outputs": [

data/example/SelectRuleByParam/SelectRuleByParam.pione CHANGED

@@ -1,25 +1,16 @@
-.@ PackageName :: "SelectRuleByParam"
-Rule Main
+Rule SelectRuleByParam
   output 'message.txt'
   param $NAME := "A"
 Flow
-  case $NAME
+    case $NAME
   when "A"
-    $RULE := A
+  rule A
   when "B"
-    $RULE := B
+  rule B
   when "C"
-    $RULE := C
+  rule C
   end
-  rule RuleSelector {R: $RULE}
-End
-Rule RuleSelector
-  output 'message.txt'
-  param $R
-Flow
-  rule $R
 End
 Rule A
@@ -39,4 +30,3 @@ Rule C
 Action
   echo "This is rule C." > {$O[1]}
 End

data/example/SelectRuleByParam/pione-package.json CHANGED

@@ -4,6 +4,7 @@
   ],
   "Documents": [
+    "Package.pione",
     "SelectRuleByParam.pione"
   ],
   "Scenarios": [
@@ -13,5 +14,8 @@
   ],
   "Bins": [
+  ],
+  "Etcs": [
   ]
 }

data/example/SequentialParameter/SequentialParameter.pione CHANGED

@@ -6,5 +6,4 @@ End
 Rule CreatedByParam
   output '{$N}.out'
-  param $N := 1.upto(10)
 End

data/example/SerialProcessing/A.pione CHANGED

@@ -1,4 +1,3 @@
 Rule A
   output '*.a'.all
 Flow

data/example/SerialProcessing/B.pione CHANGED

@@ -1,4 +1,3 @@
 Rule B
   output '*.b'.all
 Flow

data/example/SerialProcessing/SerialProcessing.pione CHANGED

@@ -1,4 +1,3 @@
 Rule SerialProcessing
   output '*.b'.all
   output '*.a'.all

data/example/SerialProcessing/pione-package.json CHANGED

@@ -4,10 +4,10 @@
   ],
   "Documents": [
+    "A.pione",
     "B.pione",
     "Package.pione",
-    "SerialProcessing.pione",
-    "A.pione"
+    "SerialProcessing.pione"
   ],
   "Scenarios": [
     "scenario"

data/example/SieveOfEratosthenes/CreateUndeterminedNumbers.pione ADDED

@@ -0,0 +1,11 @@
+Rule CreateUndeterminedNumbers
+  output '*.ud'.all
+  param $N := 2.upto($MAX)
+Flow
+  rule CreateData
+End
+Rule CreateData
+  output '{$NAME}'
+  param $NAME := "{$N}.ud"
+End

data/example/SingleParticlesWithRef/Create3dinfo.pione ADDED

@@ -0,0 +1,36 @@
+Rule Create3dinfo
+  input '{$TARGET}.ref2d'
+  input '*.roi'
+  output '{$*}.fit'
+  output '{$*}.3dinfo'
+Flow
+  rule ConvertPadToCorinfo
+  rule ConvertRoiToPad
+  rule ConvertCorinfoTo3dinfo
+End
+Rule ConvertPadToCorinfo
+  input '{$TARGET}.ref2d'
+  input '*.pad'
+  output '{$*}.corinfo'
+  output '{$*}.fit'
+Action
+  mrcImageAutoRotationCorrelation -i {$*}.pad -r {$TARGET}.ref2d -O {$*}.corinfo -fit {$*}.fit -cor {$*}.cormap -n {$nROT} -m 18 -range {$ROTMIN} {$ROTMAX} -Iter 2 -nRot2 {$nRot2} -nRot1 {$nRot1} -nRot3 {$nRot3} 2> /dev/null
+End
+Rule ConvertRoiToPad
+  input '*.roi'
+  output '{$*}.pad'
+Action
+  mrcImageWindowing -i {$*}.roi -o {$*}.mask -W 0.1 0.0 0.05 0.0 -m 18
+  mrcImagePad -i {$*}.mask -o {$*}.padtmp -W {$PAD_W} -H {$PAD_H} -m 3
+  mrcImageWindowing -i {$*}.padtmp -o {$*}.pad -W 0.1 0.0 0.1 0.0 -m 2
+End
+Rule ConvertCorinfoTo3dinfo
+  input '*.corinfo'
+  output '{$*}.3dinfo'
+Action
+  awk '/Cor/ { print $7,$16,$2,$3,$4,$5,$9,$11,$12}' {$*}.corinfo | sort -r | sed -e s/.pad/.fit/ > {$*}.3dinfolst
+  head -n 1 {$*}.3dinfolst | awk '{print $2,$3,$4,$5,$6,$1}' > {$*}.3dinfo
+End

data/example/SingleParticlesWithRef/Create3dinfo.pnml CHANGED

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--PLEASE DO NOT EDIT THIS FILE
-Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
+Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
 <pnml>
   <net type="http://www.informatik.hu-berlin.de/top/pntd/ptNetb" id="noID">
     <place id="p7">
@@ -41,7 +41,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
     </place>
     <place id="p4">
       <name>
-        <text>'*.pad'</text>
+        <text>'*.pad' #1</text>
         <graphics>
           <offset x="540" y="180"/>
         </graphics>
@@ -65,7 +65,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
     </place>
     <place id="p2">
       <name>
-        <text>&lt;'{$TARGET}.ref2d'</text>
+        <text>&lt;'{$TARGET}.ref2d' #2</text>
         <graphics>
           <offset x="540" y="250"/>
         </graphics>
@@ -80,7 +80,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
     </place>
     <place id="p1">
       <name>
-        <text>&lt;'*.roi'</text>
+        <text>&lt;'*.roi' #1</text>
         <graphics>
           <offset x="200" y="180"/>
         </graphics>
@@ -324,7 +324,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
     </arc>
     <toolspecific tool="WoPeD" version="1.0">
       <bounds>
-        <position x="2" y="22"/>
+        <position x="2" y="25"/>
         <dimension x="1905" y="784"/>
       </bounds>
       <scale>100</scale>

data/example/SingleParticlesWithRef/Package.pione CHANGED

@@ -1,3 +1,6 @@
+.@ PackageName :: "SingleParticlesWithRef"
+.@ Entrance :: SingleParticlesWithRef
 #
 # Eos for 3D reconstrucion from 2D rois using 3D initail reference
 #